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GeneBe

1-20604983-T-C

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001785.3(CDA):c.210T>C(p.Ala70=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00109 in 1,614,078 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0017 ( 6 hom., cov: 32)
Exomes 𝑓: 0.0010 ( 19 hom. )

Consequence

CDA
NM_001785.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0260
Variant links:
Genes affected
CDA (HGNC:1712): (cytidine deaminase) This gene encodes an enzyme involved in pyrimidine salvaging. The encoded protein forms a homotetramer that catalyzes the irreversible hydrolytic deamination of cytidine and deoxycytidine to uridine and deoxyuridine, respectively. It is one of several deaminases responsible for maintaining the cellular pyrimidine pool. Mutations in this gene are associated with decreased sensitivity to the cytosine nucleoside analogue cytosine arabinoside used in the treatment of certain childhood leukemias. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.61).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 1-20604983-T-C is Benign according to our data. Variant chr1-20604983-T-C is described in ClinVar as [Benign]. Clinvar id is 737822.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.026 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 6 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CDANM_001785.3 linkuse as main transcriptc.210T>C p.Ala70= synonymous_variant 2/4 ENST00000375071.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CDAENST00000375071.4 linkuse as main transcriptc.210T>C p.Ala70= synonymous_variant 2/41 NM_001785.3 P1
CDAENST00000461985.1 linkuse as main transcriptn.254T>C non_coding_transcript_exon_variant 2/33

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00171
AC:
261
AN:
152232
Hom.:
6
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00259
Gnomad EAS
AF:
0.00212
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.0182
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000647
Gnomad OTH
AF:
0.00191
GnomAD3 exomes
AF:
0.00216
AC:
543
AN:
251192
Hom.:
7
AF XY:
0.00208
AC XY:
282
AN XY:
135770
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00179
Gnomad EAS exome
AF:
0.00125
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.0175
Gnomad NFE exome
AF:
0.000810
Gnomad OTH exome
AF:
0.00505
GnomAD4 exome
AF:
0.00103
AC:
1502
AN:
1461728
Hom.:
19
Cov.:
31
AF XY:
0.00102
AC XY:
742
AN XY:
727150
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00199
Gnomad4 EAS exome
AF:
0.00526
Gnomad4 SAS exome
AF:
0.0000464
Gnomad4 FIN exome
AF:
0.0177
Gnomad4 NFE exome
AF:
0.000193
Gnomad4 OTH exome
AF:
0.00123
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00171
AC:
261
AN:
152350
Hom.:
6
Cov.:
32
AF XY:
0.00236
AC XY:
176
AN XY:
74494
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00259
Gnomad4 EAS
AF:
0.00212
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.0182
Gnomad4 NFE
AF:
0.000647
Gnomad4 OTH
AF:
0.00189
Alfa
AF:
0.000930
Hom.:
0
Bravo
AF:
0.000249
Asia WGS
AF:
0.00433
AC:
15
AN:
3478
EpiCase
AF:
0.000218
EpiControl
AF:
0.0000593

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJul 10, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.61
Cadd
Benign
3.2
Dann
Benign
0.62

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs76249360; hg19: chr1-20931476; API